AWE-CM Vectors: Augmenting Word Embeddings with a Clinical Metathesaurus

In recent years, word embeddings have been surprisingly effective at capturing intuitive characteristics of the words they represent. These vectors achieve the best results when training corpora are extremely large, sometimes billions of words. Clinical natural language processing datasets, however, tend to be much smaller. Even the largest publicly-available dataset of medical notes is three orders of magnitude smaller than the dataset of the oft-used “Google News” word vectors. In order to make up for limited training data sizes, we encode expert domain knowledge into our embeddings. Building on a previous extension of word2vec, we show that generalizing the notion of a word’s “context” to include arbitrary features creates an avenue for encoding domain knowledge into word embeddings. We show that the word vectors produced by this method outperform their textonly counterparts across the board in correlation with clinical experts.